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65 Cards in this Set

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What are the four building blocks of the cell and their larget units
sugars (polysaccharides), amino acids (proteins), fatty acids (lipids, membranes, fats), nucleotides (nucleic acid)
two kinds of nitrogenous bases (and what are they):
purines (A and G) and pyrimidine (T, U, C)
What's the difference between purines and pyrimidines?
9 memebered versus 5 membered.
Bases are linked to
sugars, generating a
molecule called a ___
nucleoside
base and sugar in nucleoside linked by which carbon and by whiuch bond?
C1 and N-glycosidic bond
Sugars in nucleosides come in one of two forms:
ribose and deoxyribose
pentose:
5-carbon sugar
Difference in DNA nad RNA's pentose:
H versus OH
A sugar + a base +
one or more phosphates
NucleoTide
what does phosphate do to the nucleotide? ___ ____
negatively charged
Nucleotides are joined (by
what kind of reaction? what is the bond formed?
condensation, phosphodiester
For our purposes, in general,
an ester bond is one that
is formed between two
__ groups with the
elimination of ___
-OH, water
non-coding sequences
introns
alternative splicing
different extrons kept in the mature MRNA to produce different versions of the same gene.
A ‘typical’ eukaryotic cell is mostly composed of: (6)
proteina, water, carbs, nucleic acid, lipids, inorganic matter.
what four elements make up 97-99% of the human body?
carbon, nitrogen, oxygen, hydrogen
force that brings non-polar molecules together
van der Waals
what is a methyl group?
Carbon surrounded by three Hydrogens
7 molecular gropus you need to know:
carboxyl, methyl, hydroxyl, amino, phosphate, carbonyl, sulfhydryl
what is a carbozyl group? Write it and Draw it
carbon connected to two oxygens (the single O is double bonded to C). Second O is bonded to a hydrogen. Bent angles between C and O's and H lies horizontal.
COOH
Draw the hydroxyl group and write it
bond, O, bond, H
Draw amino group and write it.
H2N..bent style horizontal
draw carbonyl
carbon with two bonds bent out to the left and a horizontal double bond with O the other side.
Draw sulfhydryl
bond, S, bond, hydrogen
Draw phosphate
bond, center P with 3 bonds to O's (creating so far a cross). Top O is double bonded, horizontal O has a hydrogen attached and bottom O also parallel to the other H.
The term pH is defined as
the negative logarithm to the base 10 of the hydrogen ion concentration - log10[H+]
Is the fact that a prokaryotic cell and a mitochondrion are of similar size significant in any way?
Modern Day mitochondria originated from
Bacterium.
What is SINGULARITY?
critical landmarks in cell/bio evolution.
Moore’s Law
We can squeeze twice as many transistors onto an integrated circuit every twenty-four months.
Explain how they calculated the # of calculation per second the brain can perform.
Measured retina, calculated how many edge and motion detection it can do by second mutiply it by how many times the whole body is larger than the retina,
THE SINGULARITY is derived from three overlapping technological revolutions
Genetics
Nanotechnology
Robotics (computers)
Gene products - most often ____, but increasingly ____
proteins, RNA
generally the beginnig of the gene is just the ___/___, generally 5' to transcription start. This called the ___ region.
promotor/enhancer, control.
what is the central dogma?
that there's mRNA synthesis then protein synthesis and you can't go backwards and get DNA back.
In transcription DNA has what strands?
template strand and coding strand.
What front and end does the mRNA transcript have? Why? What else needs to be done before we have mature mRNA
5' CAP and ? Poly A tail (The 5’ cap serves as a recognition signal for the translation machinery; helps protect it from degradation).
Splicing: introns removed and extrons ligated.
Summarizing the events
of mRNA maturation: (4)
1: transcription by pRNA II and capping=Primary transcript
2: Removal of 3' end nu nuclease and polyadenylation = processing intermediate.
3. endonucleolytic cleave at splice junctions.
4. ligation of exons = mature mRNA
describe idealized tRNA
clover leaf: has D loop (L) and L loop (R), anti-codon (botoom), and attached amino acid (top)
____ molecules are adaptors linking amino acids with anticodons.
tRNA
Protein synthesis: Translation initiation (10)
1) small ribosomal subunit binds to mRNA at start codon region
2)(#1 amino acid)-tRNA binds to AUG start codon.
3)Large ribosomal subunit now binds and completes the initiation complex
4) tRNA leaves A site and enters P site and next codon is positioned in A site
5)#2-tRNA binds to codon #2
6)so now both tRNA's are adjacent and their amino acids are bounded together by some enzyme in the large ribisome to form a polypeptide bond.
7) mRNA moved along and #1 tRNA ejected, etc,
8) no matching anti-codon (because its a stop codon) and release factor brought into A site.
9)signal and polypeptide relased from tRNA and tRNa ejected
10) ribosomal units separate and RF ejected.
3 words for protein tranlation summary:
initiation, elongation, and termination.
What is the general formula for an amino acid?
carboxyl group, amino group, central alpha-carbon, and the side chanin group(R).
At pH 7 ___ and ___ group are ionized in an amino acid
carboxyl and amino
Draw R group for Valine, Cysteine, and serine. Serine and Cysteine are ___ while Valine is ___
1)going up: bond, HC, CH3 to the right and CH3 on top.
2)bond, CH2, bond, SH
3)bond, central C, H to the left and on top, OH to the left.
polar, nonpolar
so peptide bond by which process?
condensation?
Thus, like nucleic acids (5’ ---> 3’), polypeptides also have ‘directionality’,
referred to as “___ to ___” (_ ---> _; they have an ____ terminus
and a ____ terminus, named by the group that is ‘free’ at each ‘end’).
amino, carboxyl
N, C
you know!
Draw a peptide bond
left to right: bond, carbon, double bonded O on top, bond, nitrogen, H below, bond.
What are the primary, secondary, tertiary, quaternary structure of a protein
1) linear sequence of amino acids
2)alpha-helix or beta-sheet (how polypeptide folds into local structures)
3) polypeptide chain (how peptide backbone, R-groups, and secondary structural features are arranged in space)
4)assembled subunits (association of individual polypeptides into a protein complex, e.g. homodimers or heterodimers)
H bonding between backbone N-H and C=O. Each peptide carbonyl is H-bonded to the N-H four residues down the chain. What is this describing?
alpha-helix from the secondary structure of a protein.
__ groups stick out from axis of alpha-helix; ___ amino acids/turn of helix.
R, 3.5
parallel or antiparallel, Can be from widely separated protein segments, H bonding between backbone N-H and C=O. What does this describe.
Beta-sheet
___ are proteins (sometimes RNA) that can catalyze a chemical reaction
enzymes
_____ needed for activity are scattered in primary sequence of a ?polypeptide?
amino acid residues
what is the mutation in sickle cell anemia?...why does this change the shpe of the red blood cell?
glutamic acid to valine. Valine in non-polar.
4 types of sequence mutations what are they?
1-silent (new codon calls for same amino acid)
2-missense/replacement (new codon calls new amino acid)
3-nonsense: enew codon is stop codon
4-framshift: extreme nonsense.
What do control regions in the DNA do?
provide information about when, where, and at what level a gene is to be transcribed
Regulation of the ______ of transcription of genes is by far the most important mechanism of gene regulation
INITIATION
In the holoenzyme: Core enzyme has ____. Sigma is _____ component----pRNA
active site, regulatory
___ binds to promotor region of DNA
sigma
So what signals control gene expression other than promotor region--think bacteria?
environmental conditions: temp, salt [], glocose/lactose.
The enzyme _____ cleaves the disaccharide lactose into the two monosaccharides ____ and ____
beta-galactosidase, galactose and glucose
What were the three experimental conditions for the E-coli experiment? Was the conclusion
lactose only, glucose only, lactose + glucose.
Enzyme only created in experiment 3: lactose only.
Besides the survival in different sugars how else were Jacques Monod and Francois Jacob gonna screen for mutant bacteria?
have ONPG present which beta-galactosidase breaks down. When broken down turns yellow and have calometric measurements done (measuring absorbance of wavelenght to determine concentration).
describe the replica plating experiment used to screen for mutant who could not grow in lactose (lacked beta-galactosidase)
have master plate with glucose only and use velvet colored black to tranfer the mutants positions on the velvet then put block on lactose only, superimpositio the position of the masterplate mutants on the lactose only mutants...see which colony dies.
In the replica plating experiment what were the 3 hypothesized reasons that the mutants could not cleave lactose.
1)lack gene for enzyme
2)lacked gene for a transporter that takes up lactose.
3)lacks an activator for transcription